Martin A.

Unless this is a distributed application, not running in CiC, just make an executable file that you run with crontab at 5:00. 

Nope.
https://invisioncommunity.com/legal/standards/#transfers
 

\IPS\Content\Search\Index::i()->index( $record ); This will add or update the item.

Wait for DOM to be loaded before doing anything in your JS. jQuery is loaded at the end of the document, which is why it isn't available at the time your PHP block is executed.
Loading a second set of jQ libraries is not the solution here.

What's your reason for adding all the entries to an array and then use that in a custom table, instead of 
$table = new \IPS\Helpers\Table\Db( 'customtable_log', $url, $where ); $table->selects = [ 'customtable_log.device', 'MAX(customtable_log.user_id) AS user_id']; $table->joins = [ [ 'select' => 'GROUP_CONCAT(DISTINCT core_members.name SEPARATOR ", ") AS shared_by', 'from' => 'core_members', 'where' => 'customtable_log.user_id = core_members.member_id' ] ]; $table->groupBy = 'COUNT(customtable_log.user_id) > 1';  ?
I haven't tested this, but you should be able to use the Db class even if you need to use a query out of the ordinary.

$recordClass::getItemsWithPermission( [ [ "`cms_custom_database_{$record::$customDatabaseId}`.`category_id`=?",$record->container()->id ] ], ... ) This should work

$( '#elMyMenu' ).on( 'menuOpened', function( elemID, originalEvent, menu ) { }); $( '#elMyMenu' ).on( 'menuClosed', function( elemID, menu ) { });  

\IPS\Output::i()->jsFiles = array_merge( \IPS\Output::i()->jsFiles, \IPS\Output::i()->js( 'admin_scriptfile.js', 'myAppName', 'admin' ) );  

But nothing here stops me from creating and sharing a regular URL for these methods, creating a GET request for it.
So I'm gonna say you do need it in every method. Or you need all state changing methods in its own controller where you run the csrfCheck regardless of request method.